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- PDB-9raz: Streptococcus pyogenes GapN in complex with NADP and glyceraldehy... -

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Basic information

Entry
Database: PDB / ID: 9raz
TitleStreptococcus pyogenes GapN in complex with NADP and glyceraldehyde-3-phosphate
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GapN / NADP / G3H / Substrate
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
GLYCERALDEHYDE-3-PHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWirsing, R. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Streptococcus pyogenes GapN in complex with NADP and glyceraldehyde-3-phosphate
Authors: Wirsing, R. / Schindelin, H.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,09316
Polymers423,6738
Non-polymers3,4208
Water71,7003980
1
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,4167
Polymers211,8374
Non-polymers1,5793
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19210 Å2
ΔGint-96 kcal/mol
Surface area60100 Å2
MethodPISA
2
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,6789
Polymers211,8374
Non-polymers1,8415
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19920 Å2
ΔGint-102 kcal/mol
Surface area59590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.150, 97.435, 100.710
Angle α, β, γ (deg.)77.060, 78.190, 68.920
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 52959.152 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4U9C786
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3980 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.43 % / Description: Prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.15-0.2 M (NH4)3-citrate 21-23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.375→48.62 Å / Num. obs: 528663 / % possible obs: 76.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.9978 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Net I/σ(I): 10.3
Reflection shellResolution: 1.375→1.481 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 26426 / CC1/2: 0.498 / Rpim(I) all: 0.518 / Rrim(I) all: 0.966 / % possible all: 19.1

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→48.62 Å / SU ML: 0.1337 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.2749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 26719 5.05 %
Rwork0.1541 501870 -
obs0.1553 528589 76.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.75 Å2
Refinement stepCycle: LAST / Resolution: 1.38→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28406 0 220 3980 32606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00630538
X-RAY DIFFRACTIONf_angle_d0.742641712
X-RAY DIFFRACTIONf_chiral_restr0.06644892
X-RAY DIFFRACTIONf_plane_restr0.00765462
X-RAY DIFFRACTIONf_dihedral_angle_d12.331311459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.390.2929770.24211188X-RAY DIFFRACTION5.47
1.39-1.410.27471030.25542016X-RAY DIFFRACTION9.21
1.41-1.420.28241720.25752858X-RAY DIFFRACTION13.21
1.42-1.440.2842160.26464075X-RAY DIFFRACTION18.58
1.44-1.460.29583080.26296182X-RAY DIFFRACTION28.16
1.46-1.480.29454950.25838861X-RAY DIFFRACTION40.57
1.48-1.50.27216110.253711918X-RAY DIFFRACTION54.25
1.5-1.530.27537010.244513924X-RAY DIFFRACTION63.41
1.53-1.550.26078170.231915574X-RAY DIFFRACTION71.3
1.55-1.570.25739310.227317440X-RAY DIFFRACTION79.66
1.57-1.60.2519890.219918991X-RAY DIFFRACTION86.58
1.6-1.630.243610970.212719988X-RAY DIFFRACTION91.85
1.63-1.660.245111080.212420668X-RAY DIFFRACTION94.41
1.66-1.70.229911100.20620859X-RAY DIFFRACTION95.29
1.7-1.730.233811780.200820896X-RAY DIFFRACTION95.64
1.73-1.770.220510890.1921000X-RAY DIFFRACTION95.84
1.77-1.820.217711240.181920919X-RAY DIFFRACTION95.86
1.82-1.870.206211520.172921125X-RAY DIFFRACTION96.14
1.87-1.920.203611500.16820909X-RAY DIFFRACTION96.06
1.92-1.980.199211700.162720966X-RAY DIFFRACTION95.9
1.98-2.050.19311730.156820972X-RAY DIFFRACTION96.11
2.05-2.140.178411140.147421053X-RAY DIFFRACTION96.29
2.14-2.230.169910830.137921234X-RAY DIFFRACTION96.79
2.23-2.350.174211230.137521301X-RAY DIFFRACTION97.23
2.35-2.50.163810780.141221347X-RAY DIFFRACTION97.22
2.5-2.690.180811010.14521266X-RAY DIFFRACTION97.13
2.69-2.960.172511470.149921270X-RAY DIFFRACTION97.11
2.96-3.390.170810590.150320990X-RAY DIFFRACTION95.84
3.39-4.270.144910850.126820555X-RAY DIFFRACTION93.8
4.27-48.620.139111580.1321525X-RAY DIFFRACTION98.43
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4720002488930.07195208826110.0009353652455390.1208445972490.09797305972580.125390190763-0.0501417353860.2747803792130.153858714663-0.01742057039160.0144692991455-0.08769692006290.009527825464230.0532102271786-0.003547766555560.121691615089-0.003822153710220.0369372486310.252329879970.05724349898320.14420080046640.3999612559-34.9384988105-9.46575876349
20.278764459795-0.1120898496490.008655730759040.116365011975-0.03995776014890.305821428841-0.03218102059230.1103581980720.3374520984910.0569788466006-0.0666433666566-0.03490669236240.01968921111480.109549380053-0.0939814489048-0.0132144178562-0.0380548153739-0.03655176641780.1011597160260.05506128124380.45001744547742.5564023043-8.2474900074214.6012546683
30.25062995891-0.0289281142998-0.00502195095590.141067857376-0.02248959720160.0669472449947-0.00483440690432-0.008423785228190.0007812068475-0.00407130819016-0.00427578615127-0.0104479127066-0.0001700368214140.00590571875401-0.002092906569630.0989565900840.00407083629060.0007642070564160.111693906689-0.009737201709650.1009788427352.1323337047-36.746789662716.0655439872
40.1403885770270.0606215012395-0.04982606206470.301328642918-0.02134156879170.0862356994915-0.0128092209585-0.04271995251720.01611482700060.0776272074939-0.0155307801822-0.05705172463380.004677379216160.0253354912864-0.01870317409750.1123036418980.0213807628759-0.009102547767020.135187732723-0.002350500004070.12586543161428.8629542775-45.440335575837.4037432482
50.2526799894020.0551288138611-0.01783187835410.193363701819-0.07097054804070.2106427274390.0319588611809-0.08979127409410.0477034087350.0576205117611-0.003259939306390.0993241897451-0.0892651306435-0.0906396220680.01919022594930.1847646159210.01191259866390.04251220051680.161414855631-0.01136008235050.132547019231-26.44055797577.34646696754-13.6011302319
60.05523565308720.0349583081213-0.03363198340810.128410531082-0.06936419667470.115576219546-0.0006133288270270.00405497695813-0.003835064639550.009165726735630.007743715868870.009587923420740.007522296732510.002654547295280.01148426417570.156152825242-0.00452425175962-0.002002132755070.109217149485-0.01571605337030.0851925528206-17.4118440455-22.7503453528-30.0477721654
70.07951490221380.0384573885779-0.01845457432460.143696711125-0.06581070026560.1592107118640.00167313128982-0.000378112679123-0.002781371251310.0271247916257-0.005500743648920.02073735369-0.0271469343941-0.01110906634960.00173720188350.1342757601580.007191536882410.0006631169609170.113866059353-0.01438304106740.0972755319127-10.29580335218.2872135347-56.0895102662
80.282735179460.12302797214-0.09465448393310.200874794245-0.01382883326590.09211451173620.0218129868088-0.0547112992632-0.05531273639990.0271575943221-0.0232773112567-0.0648486326349-0.02128016953150.0412297976684-8.20648031799E-50.129715615112-0.00727802618531-0.02062301288780.1446595603610.0116263753890.11707005889817.21614606997.15132047056-36.1356926712
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 2 through 475)AA2 - 4751 - 474
22(chain 'B' and resid 1 through 475)BC1 - 4751 - 475
33(chain 'C' and resid 1 through 475)CE1 - 4751 - 475
44(chain 'D' and resid 0 through 475)DF0 - 4751 - 476
55(chain 'E' and resid 2 through 475)EH2 - 4751 - 474
66(chain 'F' and resid 1 through 475)FJ1 - 4751 - 475
77(chain 'G' and resid 1 through 475)GO1 - 4751 - 475
88(chain 'H' and resid 0 through 475)HP0 - 4751 - 476

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